def add_get_gbif_link_entity(raw_uri):
"""Gets or adds a link_entity for a GBIF URI"""
species_id = get_gbif_species_id_from_uri(raw_uri)
uri = GBIF_BASE_URI + str(species_id)
le = LinkEntity.objects.filter(uri=uri).first()
if le:
# Already in the database
return le
api = gbifAPI()
can_name = api.get_gbif_cannonical_name(species_id)
vern_name = api.get_gbif_vernacular_name(species_id)
if not vern_name:
vern_name = can_name
print('Saving {} as {}, {}'.format(
uri,
can_name,
vern_name,
))
le = LinkEntity()
le.uri = uri
le.label = can_name
le.alt_label = vern_name
le.vocab_uri = GBIF_VOCAB_URI
le.ent_type = 'class'
le.sort = ''
le.save()
return le
def make_dinaa_link_assertions(self):
""" makes assertions to relate DINAA URIs with federal
registry documents
"""
self.make_fed_reg_vocab_entity()
fed_api = FederalRegistryAPI()
search_key_list = fed_api.get_list_cached_keyword_searches()
dinaa_matches = fed_api.get_dict_from_file(self.dinaa_matches_key)
for s_key in search_key_list:
s_json = fed_api.get_dict_from_file(s_key)
if 'results' in s_json:
for match in dinaa_matches:
for s_result in s_json['results']:
if s_result['document_number'] == match['doc']:
print('Found match for ' + match['doc'])
man_obj = False
try:
man_obj = Manifest.objects.get(
uuid=match['uuid'])
except Manifest.DoesNotExist:
man_obj = False
if man_obj is not False:
fed_uri = s_result['html_url']
le_check = False
try:
le_check = LinkEntity.objects.get(
uri=fed_uri)
except LinkEntity.DoesNotExist:
le_check = False
if le_check is False:
print('Saving entity: ' +
s_result['title'])
title = s_result['title']
if len(title) > 175:
title = title[0:175] + '...'
le = LinkEntity()
le.uri = fed_uri
le.label = title
le.alt_label = s_result['document_number']
le.vocab_uri = self.FEDERAL_REG_URI
le.ent_type = 'instance'
le.slug = 'fed-reg-docs-' + s_result[
'document_number']
le.save()
# Now save the link annotation
print('Adding ref link to ' + man_obj.label)
la = LinkAnnotation()
la.subject = man_obj.uuid
la.subject_type = man_obj.item_type
la.project_uuid = man_obj.project_uuid
la.source_id = self.source_id
la.predicate_uri = self.DC_TERMS_REF_BY
la.object_uri = fed_uri
try:
la.save()
except:
pass
def link_sites_from_filecache(self):
""" updates Open Context to save new sites
and annotations from the
file cache
"""
if self.filecache is not None:
# print('Cache update !: ' + self.cache_filekey)
self.filecache.working_dir = self.working_dir
json_obj = self.filecache.get_dict_from_file(self.cache_filekey)
if isinstance(json_obj, dict):
if 'trinomial_refs' in json_obj:
for tri_ref in json_obj['trinomial_refs']:
uri = tri_ref['rec_uri']
title = tri_ref['title']
if len(title) > 194:
title = title[0:190] + '... '
l_exists = LinkEntity.objects.filter(uri=uri)[:1]
if len(l_exists) < 1:
l_ent = LinkEntity()
l_ent.uri = uri
l_ent.label = title
l_ent.alt_label = title
l_ent.vocab_uri = tri_ref['source_uri']
l_ent.ent_type = 'class'
l_ent.save()
for trinomial in tri_ref['trinomials']:
man_objs = Manifest.objects.filter(
label=trinomial, class_uri='oc-gen:cat-site')
if len(man_objs) > 0:
man_obj = man_objs[0]
la = LinkAnnotation()
la.subject = uri # the subordinate is the subject
la.subject_type = 'uri'
la.project_uuid = man_obj.project_uuid
la.source_id = self.source_id
la.predicate_uri = "skos:broader"
la.object_uri = tri_ref['source_uri']
la.save()
try:
la.save()
except:
pass
links = LinkAnnotation.objects\
.filter(subject=man_obj.uuid,
object_uri=uri)[:1]
if len(links) < 1:
print('Link ' + man_obj.label + ' (' +
man_obj.uuid + ') to ' + uri)
la = LinkAnnotation()
la.subject = man_obj.uuid # the subordinate is the subject
la.subject_type = man_obj.item_type
la.project_uuid = man_obj.project_uuid
la.source_id = self.source_id
la.predicate_uri = 'dc-terms:isReferencedBy'
la.object_uri = uri
la.save()
try:
la.save()
except:
pass
def add_missing_containing_regions(project_uuid='0', source_id=SOURCE_ID):
"""Adds missing containing regions that have site counts"""
for state, state_uuid, new_region, new_uuid, geonames_uri in ADD_REGIONS:
row = {
'parent_uuid': state_uuid,
'context_uuid': new_uuid,
'label': new_region,
'class_uri': 'oc-gen:cat-region',
}
load_context_row(project_uuid=project_uuid,
source_id=source_id,
row=row)
ent_exists = LinkEntity.objects.filter(uri=geonames_uri).first()
if not ent_exists:
ent = LinkEntity()
ent.uri = geonames_uri
ent.label = new_region
ent.alt_label = new_region
ent.vocab_uri = GeonamesAPI().VOCAB_URI
ent.ent_type = 'class'
ent.save()
la_exists = LinkAnnotation.objects.filter(
subject=new_uuid, object_uri=geonames_uri).first()
if not la_exists:
new_la = LinkAnnotation()
new_la.subject = new_uuid
new_la.subject_type = 'subjects'
new_la.project_uuid = project_uuid
new_la.source_id = source_id
new_la.predicate_uri = 'skos:closeMatch'
new_la.object_uri = geonames_uri
new_la.creator_uuid = ''
new_la.save()
def find_related_geonames(self, username='******'):
""" Adds geonames spatial data for items with geonames annotations """
man_objs = Manifest.objects\
.filter(project_uuid='0',
class_uri='oc-gen:cat-region',
item_type='subjects')
for man_obj in man_objs:
print('Checking slug: ' + man_obj.slug)
subj_obj = Subject.objects.get(uuid=man_obj.uuid)
context = subj_obj.context
if '/' in context:
cont_ex = context.split('/')
admin_level = len(cont_ex) - 1
if admin_level < 0:
admin_level = 0
else:
admin_level = 0
q_str = context.replace('/', ' ')
geo_api = GeonamesAPI()
json_r = geo_api.search_admin_entity(q_str, admin_level, username)
if isinstance(json_r, dict):
# we found a result from GeoNames!
print('Geonames result found.')
if 'geonames' in json_r:
if len(json_r['geonames']) > 0:
# we've got a result
geo_id = json_r['geonames'][0]['geonameId']
label = json_r['geonames'][0]['name']
alt_label = json_r['geonames'][0]['toponymName']
geonames_uri = 'http://www.geonames.org/' + str(geo_id)
l_ents = LinkEntity.objects\
.filter(uri=geonames_uri)[:1]
if len(l_ents) < 1:
# we need to create this entity
ent = LinkEntity()
ent.uri = geonames_uri
ent.label = label
ent.alt_label = alt_label
ent.vocab_uri = GeonamesAPI().VOCAB_URI
ent.ent_type = 'class'
ent.save()
print(geonames_uri)
annos = LinkAnnotation.objects\
.filter(subject=man_obj.uuid,
object_uri=geonames_uri)[:1]
if len(annos) < 1:
# we need to add the annotation linking this item
print('Adding new annotation!')
new_la = LinkAnnotation()
new_la.subject = man_obj.uuid
new_la.subject_type = man_obj.item_type
new_la.project_uuid = man_obj.project_uuid
new_la.source_id = man_obj.source_id
new_la.predicate_uri = 'skos:closeMatch'
new_la.object_uri = geonames_uri
new_la.creator_uuid = ''
new_la.save()
else:
print('Relation already known.')
def save_csv_from_filecache(self):
""" updates Open Context to save new sites
and annotations from the
file cache
"""
if self.filecache is not None:
# print('Cache update !: ' + self.cache_filekey)
self.filecache.working_dir = self.working_dir
json_obj = self.filecache.get_dict_from_file(self.cache_filekey)
filename = self.cache_filekey + '.csv'
directory = self.filecache.prep_directory(self.working_dir)
dir_filename = os.path.join(directory, filename)
if isinstance(json_obj, dict):
if 'trinomial_refs' in json_obj:
field_name_row = [
'County Code', 'County Name', 'Trinomial', 'Citation',
'URI', 'Title', 'Note'
]
f = codecs.open(dir_filename, 'w', encoding='utf-8')
writer = csv.writer(f,
dialect=csv.excel,
quoting=csv.QUOTE_ALL)
writer.writerow(field_name_row)
for tri_ref in json_obj['trinomial_refs']:
citation = tri_ref['citation_html']
uri = tri_ref['rec_uri']
title = tri_ref['title']
if len(title) > 194:
title = title[0:190] + '... '
l_exists = LinkEntity.objects.filter(uri=uri)[:0]
if len(l_exists) < 1:
l_ent = LinkEntity()
l_ent.uri = uri
l_ent.label = title
l_ent.alt_label = title
l_ent.vocab_uri = tri_ref['source_uri']
l_ent.ent_type = 'class'
l_ent.save()
if 'note' in tri_ref:
note = tri_ref['note']
else:
note = ''
for trinomial in tri_ref['trinomials']:
county_code = trinomial[0:4]
act_county_name = None
for key, county_name in self.COUNTY_PREFIXES.items(
):
if county_code == key:
act_county_name = county_name
break
print('County code: ' + county_code + ' is ' +
str(act_county_name))
row = [
county_code, act_county_name, trinomial,
citation, uri, title, note
]
writer.writerow(row)
print('Done!')
f.closed
def save_entity_labels(self):
""" saves labels of entities in a vocabulary """
output = False
if self.graph is not False and self.vocabulary_uri is not False:
output = []
if self.replace_old:
LinkEntity.objects.filter(vocab_uri=self.vocabulary_uri).delete()
for s, p, o in self.graph.triples((None,
RDFS.label,
None)):
subject_uri = s.__str__() # get the URI of the subject as a string
label = o.__str__() # get the Label of from object as a string
le_ents = LinkEntity.objects.filter(uri=subject_uri)[:1]
if len(le_ents) < 1 or self.replace_old:
newr = LinkEntity()
newr.uri = subject_uri
newr.label = label
newr.alt_label = label
newr.ent_type = 'class'
newr.vocab_uri = self.vocabulary_uri
newr.save()
act_t = {'s': subject_uri,
'o': label}
output.append(act_t)
return output
def link_sites_from_filecache(self):
""" updates Open Context to save new sites
and annotations from the
file cache
"""
if self.filecache is not None:
# print('Cache update !: ' + self.cache_filekey)
self.filecache.working_dir = self.working_dir
json_obj = self.filecache.get_dict_from_file(self.cache_filekey)
if isinstance(json_obj, dict):
if 'trinomial_refs' in json_obj:
for tri_ref in json_obj['trinomial_refs']:
uri = tri_ref['rec_uri']
title = tri_ref['title']
if len(title) > 194:
title = title[0:190] + '... '
l_exists = LinkEntity.objects.filter(uri=uri)[:1]
if len(l_exists) < 1:
l_ent = LinkEntity()
l_ent.uri = uri
l_ent.label = title
l_ent.alt_label = title
l_ent.vocab_uri = tri_ref['source_uri']
l_ent.ent_type = 'class'
l_ent.save()
for trinomial in tri_ref['trinomials']:
man_objs = Manifest.objects.filter(label=trinomial,
class_uri='oc-gen:cat-site')
if len(man_objs) > 0:
man_obj = man_objs[0]
la = LinkAnnotation()
la.subject = uri # the subordinate is the subject
la.subject_type = 'uri'
la.project_uuid = man_obj.project_uuid
la.source_id = self.source_id
la.predicate_uri = "skos:broader"
la.object_uri = tri_ref['source_uri']
la.save()
try:
la.save()
except:
pass
links = LinkAnnotation.objects\
.filter(subject=man_obj.uuid,
object_uri=uri)[:1]
if len(links) < 1:
print('Link ' + man_obj.label + ' (' + man_obj.uuid + ') to ' + uri)
la = LinkAnnotation()
la.subject = man_obj.uuid # the subordinate is the subject
la.subject_type = man_obj.item_type
la.project_uuid = man_obj.project_uuid
la.source_id = self.source_id
la.predicate_uri = 'dc-terms:isReferencedBy'
la.object_uri = uri
la.save()
try:
la.save()
except:
pass
def make_fed_reg_vocab_entity(self):
""" makes a vocabulary entity for the federal registry """
try:
le_check = LinkEntity.objects.get(uri=self.FEDERAL_REG_URI)
except LinkEntity.DoesNotExist:
le_check = False
if le_check is False:
le = LinkEntity()
le.uri = self.FEDERAL_REG_URI
le.label = self.FEDERAL_REG_LABEL
le.alt_label = self.FEDERAL_REG_LABEL
le.vocab_uri = self.FEDERAL_REG_URI
le.ent_type = 'vocabulary'
le.slug = 'fed-reg'
le.save()
def check_add_periodo_vocab(self):
""" Adds the periodo vocabulary if it doesn't exist yet
"""
lev = LinkEntity.objects.filter(uri=self.PERIODO_VOCAB_URI)[:1]
if len(lev) < 1:
le = LinkEntity()
le.uri = self.PERIODO_VOCAB_URI
le.label = 'PeriodO'
le.alt_label = 'PeriodO (http://perio.do)'
le.vocab_uri = self.PERIODO_VOCAB_URI
le.ent_type = 'vocabulary'
le.save()
def make_dinaa_link_assertions(self):
""" makes assertions to relate DINAA URIs with federal
registry documents
"""
self.make_fed_reg_vocab_entity()
fed_api = FederalRegistryAPI()
search_key_list = fed_api.get_list_cached_keyword_searches()
dinaa_matches = fed_api.get_dict_from_file(self.dinaa_matches_key)
for s_key in search_key_list:
s_json = fed_api.get_dict_from_file(s_key)
if 'results' in s_json:
for match in dinaa_matches:
for s_result in s_json['results']:
if s_result['document_number'] == match['doc']:
print('Found match for ' + match['doc'])
man_obj = False
try:
man_obj = Manifest.objects.get(uuid=match['uuid'])
except Manifest.DoesNotExist:
man_obj = False
if man_obj is not False:
fed_uri = s_result['html_url']
le_check = False
try:
le_check = LinkEntity.objects.get(uri=fed_uri)
except LinkEntity.DoesNotExist:
le_check = False
if le_check is False:
print('Saving entity: ' + s_result['title'])
title = s_result['title']
if len(title) > 175:
title = title[0:175] + '...'
le = LinkEntity()
le.uri = fed_uri
le.label = title
le.alt_label = s_result['document_number']
le.vocab_uri = self.FEDERAL_REG_URI
le.ent_type = 'instance'
le.slug = 'fed-reg-docs-' + s_result['document_number']
le.save()
# Now save the link annotation
print('Adding ref link to ' + man_obj.label)
la = LinkAnnotation()
la.subject = man_obj.uuid
la.subject_type = man_obj.item_type
la.project_uuid = man_obj.project_uuid
la.source_id = self.source_id
la.predicate_uri = self.DC_TERMS_REF_BY
la.object_uri = fed_uri
try:
la.save()
except:
pass
def validate_fix_eol_objects(self):
""" Searches for EOL links in the
LinkAnnotations table, then fixes
badly URIs with cruft. Also
calls the EOL API to get labels
for URIs with no record in the LinkEntity
table.
"""
checked_uris = []
eol_las = LinkAnnotation.objects\
.filter(object_uri__icontains=self.EOL_URI_PREFIX)
for eol_la in eol_las:
eol_uri = eol_la.object_uri
leg = LinkEntityGeneration()
le_gen = LinkEntityGeneration()
eol_uri = le_gen.make_clean_uri(
eol_uri) # strip off any cruft in the URI
if eol_uri != eol_la.object_uri:
print('Has cruft: ' + str(eol_la.object_uri))
LinkAnnotation.objects\
.filter(hash_id=eol_la.hash_id)\
.delete() # delete the old
eol_la.object_uri = eol_uri
eol_la.save() # save the cleaned URI
if eol_uri not in checked_uris:
# only check on a given URI once
checked_uris.append(eol_uri)
try:
le = LinkEntity.objects.get(uri=eol_uri)
except LinkEntity.DoesNotExist:
le = False
if le is False:
print('Getting missing data for: ' + eol_uri)
label = False
eol_api = eolAPI()
eol_data = eol_api.get_basic_json_for_eol_uri(eol_uri)
if isinstance(eol_data, dict):
print('Reading data...')
if 'scientificName' in eol_data:
label = eol_data['scientificName']
else:
print('Failed to read data: ' + str(eol_data))
if label is not False:
print('Saving data for: ' + str(label) + ' (' +
eol_uri + ')')
le = LinkEntity()
le.uri = eol_uri
le.label = label
le.alt_label = label
le.ent_type = 'class'
le.vocab_uri = self.EOL_VOCAB_URI
le.save()
def check_add_period_pred(self):
""" Adds the periodo vocabulary if it doesn't exist yet
"""
temporal_pred = 'http://purl.org/dc/terms/temporal'
lev = LinkEntity.objects.filter(uri=temporal_pred)[:1]
if len(lev) < 1:
le = LinkEntity()
le.uri = temporal_pred
le.label = 'Temporal Coverage'
le.alt_label = 'Temporal Coverage'
le.vocab_uri = 'http://purl.org/dc/terms'
le.ent_type = 'property'
le.save()
def make_fed_reg_vocab_entity(self):
""" makes a vocabulary entity for the federal registry """
try:
le_check = LinkEntity.objects.get(uri=self.FEDERAL_REG_URI)
except LinkEntity.DoesNotExist:
le_check = False
if le_check is False:
le = LinkEntity()
le.uri = self.FEDERAL_REG_URI
le.label = self.FEDERAL_REG_LABEL
le.alt_label = self.FEDERAL_REG_LABEL
le.vocab_uri = self.FEDERAL_REG_URI
le.ent_type = 'vocabulary'
le.slug = 'fed-reg'
le.save()
def check_add_period(self, p_ref):
""" Checks to see if a period collection is in
the database, adds it if needed
"""
if not p_ref['period-meta']['uri'] in self.db_uris:
# not in memory for being in the database
lev = LinkEntity.objects.filter(
uri=p_ref['period-meta']['uri'])[:1]
if len(lev) < 1 or self.update_period:
le = LinkEntity()
le.uri = p_ref['period-meta']['uri']
le.label = p_ref['period-meta']['label-range']
le.alt_label = p_ref['period-meta']['label']
le.vocab_uri = p_ref['collection']['uri']
le.ent_type = 'class'
le.save()
self.db_uris.append(p_ref['period-meta']['uri'])
def validate_fix_uberon_objects(self):
""" Searches for UBERON links in the
LinkAnnotations table, then fixes
badly URIs with cruft. Also
calls the UBERON API to get labels
for URIs with no record in the LinkEntity
table.
"""
checked_uris = []
uberon_las = LinkAnnotation.objects\
.filter(object_uri__icontains=self.UBERON_URI_PREFIX)
for uberon_la in uberon_las:
uberon_uri = uberon_la.object_uri
le_gen = LinkEntityGeneration()
uberon_uri = le_gen.make_clean_uri(
uberon_uri) # strip off any cruft in the URI
if uberon_uri != uberon_la.object_uri:
print('Has cruft: ' + str(uberon_la.object_uri))
LinkAnnotation.objects\
.filter(hash_id=uberon_la.hash_id)\
.delete() # delete the old
uberon_la.object_uri = uberon_uri
uberon_la.save() # save the cleaned URI
if uberon_uri not in checked_uris:
# only check on a given URI once
checked_uris.append(uberon_uri)
try:
le = LinkEntity.objects.get(uri=uberon_uri)
except LinkEntity.DoesNotExist:
le = False
if le is False:
print('Getting missing data for: ' + uberon_uri)
u_api = uberonAPI()
label = u_api.get_uri_label_from_graph(uberon_uri)
if label is False:
print('Failed to read data for : ' + str(uberon_uri))
else:
print('Saving data for: ' + str(label) + ' (' +
uberon_uri + ')')
le = LinkEntity()
le.uri = uberon_uri
le.label = label
le.alt_label = label
le.ent_type = 'class'
le.vocab_uri = self.UBERON_VOCAB_URI
le.save()
def check_add_period_collection(self, p_ref):
""" Checks to see if a period collection is in
the database, adds it if needed
"""
if not p_ref['collection']['uri'] in self.db_uris:
# not in memory for being in the database
lev = LinkEntity.objects.filter(uri=p_ref['collection']['uri'])[:1]
if len(lev) < 1:
le = LinkEntity()
le.uri = p_ref['collection']['uri']
le.label = 'PeriodO Collection: ' + p_ref['collection']['label']
le.alt_label = 'PeriodO (http://perio.do): ' + p_ref[
'collection']['label']
le.vocab_uri = self.PERIODO_VOCAB_URI
le.ent_type = 'vocabulary'
le.save()
self.db_uris.append(p_ref['collection']['uri'])
def store_records(self, act_table, recs):
"""
stores records retrieved for a given table
"""
i = 0
for record in recs:
i += 1
allow_write = self.check_allow_write(act_table, record)
record = self.prep_update_keep_old(act_table, record)
if (allow_write is False and self.update_keep_old is False):
print('\n Not allowed to overwite record.' + str(i))
else:
# print('\n Adding record:' + str(record))
newr = False
if (act_table == 'link_annotations'):
newr = LinkAnnotation(**record)
elif (act_table == 'link_entities'):
newr = LinkEntity(**record)
elif (act_table == 'oc_assertions'):
newr = Assertion(**record)
elif (act_table == 'oc_manifest'):
newr = Manifest(**record)
elif (act_table == 'oc_subjects'):
newr = Subject(**record)
elif (act_table == 'oc_mediafiles'):
newr = Mediafile(**record)
elif (act_table == 'oc_documents'):
newr = OCdocument(**record)
elif (act_table == 'oc_persons'):
newr = Person(**record)
elif (act_table == 'oc_projects'):
newr = Project(**record)
elif (act_table == 'oc_strings'):
newr = OCstring(**record)
elif (act_table == 'oc_types'):
newr = OCtype(**record)
elif (act_table == 'oc_geospace'):
newr = Geospace(**record)
elif (act_table == 'oc_events'):
newr = Event(**record)
elif (act_table == 'oc_predicates'):
newr = Predicate(**record)
elif (act_table == 'oc_identifiers'):
newr = StableIdentifer(**record)
elif (act_table == 'oc_obsmetadata'):
newr = ObsMetadata(**record)
if (newr is not False):
try:
newr.save(force_insert=self.force_insert,
force_update=self.update_keep_old)
except Exception as error:
print('Something slipped past in ' + act_table +
'...' + str(error))
def check_add_period(self, p_ref, vocab_uri):
""" Checks to see if a period collection is in
the database, adds it if needed
"""
if isinstance(p_ref, dict):
uri = PeriodoAPI.URI_PREFIX + p_ref['id']
if not uri in self.db_uris:
# not in memory for being in the database
lev = LinkEntity.objects.filter(uri=uri)[:1]
if len(lev) < 1 or self.update_period:
le = LinkEntity()
le.uri = uri
le.label = p_ref['label']
le.alt_label = p_ref['alt_label']
le.vocab_uri = vocab_uri
le.ent_type = 'class'
le.save()
self.db_uris.append(uri)
def check_add_period_collection(self, p_ref):
""" Checks to see if a period collection is in
the database, adds it if needed
"""
if isinstance(p_ref, dict):
uri = PeriodoAPI.URI_PREFIX + p_ref['id']
if not uri in self.db_uris:
# not in memory for being in the database
lev = LinkEntity.objects.filter(uri=uri)[:1]
if len(lev) < 1 or self.update_period:
le = LinkEntity()
le.uri = uri
le.label = 'PeriodO Collection: ' + p_ref['source']['title']
le.alt_label = 'PeriodO (http://perio.do): ' + p_ref['source']['title']
le.vocab_uri = self.PERIODO_VOCAB_URI
le.ent_type = 'vocabulary'
le.save()
self.db_uris.append(uri)
def store_records(self, act_table, recs):
"""
stores records retrieved for a given table
"""
for rkey, record in recs.items():
if (act_table == 'link_annotations'):
newr = LinkAnnotation(**record)
newr.save()
elif (act_table == 'link_entities'):
newr = LinkEntity(**record)
newr.save()
elif (act_table == 'link_hierarchies'):
newr = LinkHierarchy(**record)
newr.save()
elif (act_table == 'oc_chronology'):
newr = Chronology(**record)
newr.save()
elif (act_table == 'oc_geodata'):
newr = Geodata(**record)
newr.save()
elif (act_table == 'oc_mediafiles'):
newr = Mediafile(**record)
newr.save()
elif (act_table == 'oc_documents'):
newr = OCdocument(**record)
newr.save()
elif (act_table == 'oc_persons'):
newr = Person(**record)
newr.save()
elif (act_table == 'oc_projects'):
newr = Project(**record)
newr.save()
elif (act_table == 'oc_strings'):
newr = OCstring(**record)
newr.save()
elif (act_table == 'oc_types'):
newr = OCtype(**record)
newr.save()
elif (act_table == 'oc_events'):
newr = Event(**record)
newr.save()
elif (act_table == 'oc_predicates'):
newr = Predicate(**record)
newr.save()
elif (act_table == 'oc_identifiers'):
newr = StableIdentifer(**record)
newr.save()
elif (act_table == 'oc_obsmetadata'):
newr = ObsMetadata(**record)
newr.save()
def validate_fix_eol_objects(self):
""" Searches for EOL links in the
LinkAnnotations table, then fixes
badly URIs with cruft. Also
calls the EOL API to get labels
for URIs with no record in the LinkEntity
table.
"""
checked_uris = []
eol_las = LinkAnnotation.objects.filter(object_uri__icontains=self.EOL_URI_PREFIX)
for eol_la in eol_las:
eol_uri = eol_la.object_uri
leg = LinkEntityGeneration()
le_gen = LinkEntityGeneration()
eol_uri = le_gen.make_clean_uri(eol_uri) # strip off any cruft in the URI
if eol_uri != eol_la.object_uri:
print("Has cruft: " + str(eol_la.object_uri))
LinkAnnotation.objects.filter(hash_id=eol_la.hash_id).delete() # delete the old
eol_la.object_uri = eol_uri
eol_la.save() # save the cleaned URI
if eol_uri not in checked_uris:
# only check on a given URI once
checked_uris.append(eol_uri)
try:
le = LinkEntity.objects.get(uri=eol_uri)
except LinkEntity.DoesNotExist:
le = False
if le is False:
print("Getting missing data for: " + eol_uri)
label = False
eol_api = eolAPI()
eol_data = eol_api.get_basic_json_for_eol_uri(eol_uri)
if isinstance(eol_data, dict):
print("Reading data...")
if "scientificName" in eol_data:
label = eol_data["scientificName"]
else:
print("Failed to read data: " + str(eol_data))
if label is not False:
print("Saving data for: " + str(label) + " (" + eol_uri + ")")
le = LinkEntity()
le.uri = eol_uri
le.label = label
le.alt_label = label
le.ent_type = "class"
le.vocab_uri = self.EOL_VOCAB_URI
le.save()
def validate_fix_uberon_objects(self):
""" Searches for UBERON links in the
LinkAnnotations table, then fixes
badly URIs with cruft. Also
calls the UBERON API to get labels
for URIs with no record in the LinkEntity
table.
"""
checked_uris = []
uberon_las = LinkAnnotation.objects\
.filter(object_uri__icontains=self.UBERON_URI_PREFIX)
for uberon_la in uberon_las:
uberon_uri = uberon_la.object_uri
le_gen = LinkEntityGeneration()
uberon_uri = le_gen.make_clean_uri(uberon_uri) # strip off any cruft in the URI
if uberon_uri != uberon_la.object_uri:
print('Has cruft: ' + str(uberon_la.object_uri))
LinkAnnotation.objects\
.filter(hash_id=uberon_la.hash_id)\
.delete() # delete the old
uberon_la.object_uri = uberon_uri
uberon_la.save() # save the cleaned URI
if uberon_uri not in checked_uris:
# only check on a given URI once
checked_uris.append(uberon_uri)
try:
le = LinkEntity.objects.get(uri=uberon_uri)
except LinkEntity.DoesNotExist:
le = False
if le is False:
print('Getting missing data for: ' + uberon_uri)
u_api = uberonAPI()
label = u_api.get_uri_label_from_graph(uberon_uri)
if label is False:
print('Failed to read data for : ' + str(uberon_uri))
else:
print('Saving data for: ' + str(label) + ' (' + uberon_uri + ')')
le = LinkEntity()
le.uri = uberon_uri
le.label = label
le.alt_label = label
le.ent_type = 'class'
le.vocab_uri = self.UBERON_VOCAB_URI
le.save()
def get_save_entity_label(self, eol_uri):
""" gets the entity label from the EOL API
and saves it
"""
label = False
eol_api = eolAPI()
eol_data = eol_api.get_basic_json_for_eol_uri(eol_uri)
if isinstance(eol_data, dict):
print('Reading data...')
if 'scientificName' in eol_data:
label = eol_data['scientificName']
else:
print('Failed to read data: ' + str(eol_data))
if label is not False:
print('Saving data for: ' + str(label) + ' (' + eol_uri + ')')
le = LinkEntity()
le.uri = eol_uri
le.label = label
le.alt_label = label
le.ent_type = 'class'
le.vocab_uri = self.EOL_VOCAB_URI
le.save()
def save_entity_labels(self):
""" saves labels of entities in a vocabulary """
output = False
if (self.graph is not False and self.vocabulary_uri is not False):
output = []
if (self.replace_old):
LinkEntity.objects.filter(
vocab_uri=self.vocabulary_uri).delete()
for s, p, o in self.graph.triples((None, RDFS.label, None)):
subject_uri = s.__str__(
) # get the URI of the subject as a string
label = o.__str__() # get the Label of the object as a string
newr = LinkEntity()
newr.uri = subject_uri
newr.label = label
newr.alt_label = label
newr.ent_type = 'type'
newr.vocab_uri = self.vocabulary_uri
newr.save()
act_t = {'s': subject_uri, 'o': label}
output.append(act_t)
return output
def get_save_entity_label(self, eol_uri):
""" gets the entity label from the EOL API
and saves it
"""
label = False
eol_api = eolAPI()
eol_data = eol_api.get_basic_json_for_eol_uri(eol_uri)
if isinstance(eol_data, dict):
print('Reading data...')
if 'scientificName' in eol_data:
label = eol_data['scientificName']
else:
print('Failed to read data: ' + str(eol_data))
if label is not False:
print('Saving data for: ' + str(label) + ' (' + eol_uri + ')')
le = LinkEntity()
le.uri = eol_uri
le.label = label
le.alt_label = label
le.ent_type = 'class'
le.vocab_uri = self.EOL_VOCAB_URI
le.save()
def check_add_link_entity(self, uri):
""" Checks to see if an entity exists, if not, it adds
it if we recognize the URI to be part of a
known vocabulary
"""
ent = LinkEntity.objects.filter(uri=uri).first()
if ent:
# We found the linked data entity.
return ent
label = None
alt_label = None
ent_type = 'class'
vocab_uri = None
if '.geonames.org' in uri:
geo_api = GeonamesAPI()
vocab_uri = GeonamesAPI().VOCAB_URI
labels = geo_api.get_labels_for_uri(uri)
if isinstance(labels, dict):
# got the label!
label = labels['label']
alt_label = labels['alt_label']
elif 'UBERON' in uri:
uber_api = uberonAPI()
vocab_uri = uberonAPI().VOCAB_URI
label = uber_api.get_uri_label_from_graph(uri)
if label is not False:
alt_label = label
elif 'eol.org' in uri:
eol_api = eolAPI()
vocab_uri = eolAPI().VOCAB_URI
labels = eol_api.get_labels_for_uri(uri)
if isinstance(labels, dict):
# got the label!
label = labels['label']
alt_label = labels['alt_label']
elif 'wikipedia.org' in uri:
# page name in the URI of the article
link_ex = uri.split('/')
label = urlunquote(link_ex[-1])
label = label.replace('_', ' ') # underscores in Wikipedia titles
alt_label = label
vocab_uri = 'http://www.wikipedia.org/'
elif 'vocab.getty.edu/aat' in uri:
print('Finding: ' + uri)
getty_api = gettyAPI()
vocab_uri = gettyAPI().VOCAB_URI
labels = getty_api.get_labels_for_uri(uri)
if isinstance(labels, dict):
# got the label!
label = labels['label']
alt_label = labels['alt_label']
elif 'numismatics.org/ocre/id/' in uri:
print('Finding: ' + uri)
ANSochre = ANSochreAPI()
vocab_uri = ANSochreAPI().VOCAB_URI
labels = ANSochre.get_labels_for_uri(uri)
if isinstance(labels, dict):
# got the label!
label = labels['label']
alt_label = labels['alt_label']
elif 'gbif.org/species/' in uri:
ent = add_get_gbif_link_entity_and_hierarchy(uri)
# This adds the linked entity to the database
# as well as its hierarchy
return ent
if not label or not vocab_uri:
# Something went wrong. Could not
# add the item
return None
# ok to make an entity then!
ent = LinkEntity()
ent.uri = uri
ent.label = label
ent.alt_label = alt_label
ent.vocab_uri = vocab_uri
ent.ent_type = ent_type
ent.sort = ''
ent.save()
return ent
def save_csv_from_filecache(self):
""" updates Open Context to save new sites
and annotations from the
file cache
"""
if self.filecache is not None:
# print('Cache update !: ' + self.cache_filekey)
self.filecache.working_dir = self.working_dir
json_obj = self.filecache.get_dict_from_file(self.cache_filekey)
filename = self.cache_filekey + '.csv'
directory = self.filecache.prep_directory(self.working_dir)
dir_filename = os.path.join(directory,
filename)
if isinstance(json_obj, dict):
if 'trinomial_refs' in json_obj:
field_name_row = [
'County Code',
'County Name',
'Trinomial',
'Citation',
'URI',
'Title',
'Note'
]
f = codecs.open(dir_filename, 'w', encoding='utf-8')
writer = csv.writer(f, dialect=csv.excel, quoting=csv.QUOTE_ALL)
writer.writerow(field_name_row)
for tri_ref in json_obj['trinomial_refs']:
citation = tri_ref['citation_html']
uri = tri_ref['rec_uri']
title = tri_ref['title']
if len(title) > 194:
title = title[0:190] + '... '
l_exists = LinkEntity.objects.filter(uri=uri)[:0]
if len(l_exists) < 1:
l_ent = LinkEntity()
l_ent.uri = uri
l_ent.label = title
l_ent.alt_label = title
l_ent.vocab_uri = tri_ref['source_uri']
l_ent.ent_type = 'class'
l_ent.save()
if 'note' in tri_ref:
note = tri_ref['note']
else:
note = ''
for trinomial in tri_ref['trinomials']:
county_code = trinomial[0:4]
act_county_name = None
for key, county_name in self.COUNTY_PREFIXES.items():
if county_code == key:
act_county_name = county_name
break
print('County code: ' + county_code + ' is ' + str(act_county_name))
row = [
county_code,
act_county_name,
trinomial,
citation,
uri,
title,
note
]
writer.writerow(row)
print('Done!')
f.closed
def add_update(self, post_data):
""" Creates or updates a linked data entity """
ok = True
uri = False
label = False
vocab_uri = False
alt_label = False
ent_type = 'class'
note = ''
action = 'attempted creation or update'
sent_uri = uri
sent_label = label
if 'uri' in post_data:
uri = post_data['uri']
sent_uri = uri
if not self.validate_web_uri(uri):
# must be a full web uri to use
note += '"' + uri + '" needs to be valid Web URI. '
uri = False
if 'label' in post_data:
label = post_data['label']
sent_label = label
alt_label = label # default for alt-label is label
if len(label) < 1:
note += 'The entity label cannot be blank. '
label = False
if 'alt_label' in post_data:
if len(post_data['alt_label']) > 0:
alt_label = post_data['alt_label']
if 'ent_type' in post_data:
ent_type = post_data['ent_type']
if 'vocab_uri' in post_data:
vocab_uri = post_data['vocab_uri']
if not self.validate_web_uri(vocab_uri)\
and ent_type != 'vocabulary':
# vocab_uri is not a full uri, so suggest one
# based on the URI for the request
vocab_uri = self.suggest_vocabulary(uri)
elif not self.validate_web_uri(vocab_uri)\
and ent_type == 'vocabulary':
vocab_uri = uri
else:
pass
if uri is not False \
and label is not False \
and vocab_uri is not False:
le_gen = LinkEntityGeneration()
uri = le_gen.make_clean_uri(uri)
if uri != vocab_uri:
# get the varient of the vocab_uri that's actually in use
# returns false if a varient can't be found
vocab_uri = self.check_vocab_uri(vocab_uri)
if vocab_uri is False:
# cannot find a varient for this vocabulary uri
vocab_ok = False
else:
vocab_ok = True
elif ent_type == 'vocabulary':
vocab_ok = True
else:
vocab_ok = False
if vocab_ok:
ok = True
try:
action = 'edit-update'
le = LinkEntity.objects.get(uri=uri)
except LinkEntity.DoesNotExist:
action = 'add-create'
le = LinkEntity()
le.uri = uri
# now add information to save
le.label = label
le.alt_label = alt_label
le.ent_type = ent_type
le.vocab_uri = vocab_uri
le.save()
uri = le.uri # in case the URI changed because of validation changes
else:
ok = False
note += 'Must first create a record for the vocabulary. '
else:
ok = False
note += 'Missing data required for this action. '
self.response = {
'action': action,
'uri': sent_uri,
'label': sent_label,
'ok': ok,
'change': {
'note': note
}
}
return self.response
def find_related_geonames(self, username='******'):
""" Adds geonames spatial data for items with geonames annotations """
man_objs = Manifest.objects\
.filter(project_uuid='0',
class_uri='oc-gen:cat-region',
item_type='subjects')
for man_obj in man_objs:
print('Checking slug: ' + man_obj.slug)
subj_obj = Subject.objects.get(uuid=man_obj.uuid)
context = subj_obj.context
if '/' in context:
cont_ex = context.split('/')
admin_level = len(cont_ex) - 1
if admin_level < 0:
admin_level = 0
else:
admin_level = 0
q_str = context.replace('/', ' ')
geo_api = GeonamesAPI()
json_r = geo_api.search_admin_entity(q_str,
admin_level,
username)
if isinstance(json_r, dict):
# we found a result from GeoNames!
print('Geonames result found.')
if 'geonames' in json_r:
if len(json_r['geonames']) > 0:
# we've got a result
geo_id = json_r['geonames'][0]['geonameId']
label = json_r['geonames'][0]['name']
alt_label = json_r['geonames'][0]['toponymName']
geonames_uri = 'http://www.geonames.org/' + str(geo_id)
l_ents = LinkEntity.objects\
.filter(uri=geonames_uri)[:1]
if len(l_ents) < 1:
# we need to create this entity
ent = LinkEntity()
ent.uri = geonames_uri
ent.label = label
ent.alt_label = alt_label
ent.vocab_uri = GeonamesAPI().VOCAB_URI
ent.ent_type = 'class'
ent.save()
print(geonames_uri)
annos = LinkAnnotation.objects\
.filter(subject=man_obj.uuid,
object_uri=geonames_uri)[:1]
if len(annos) < 1:
# we need to add the annotation linking this item
print('Adding new annotation!')
new_la = LinkAnnotation()
new_la.subject = man_obj.uuid
new_la.subject_type = man_obj.item_type
new_la.project_uuid = man_obj.project_uuid
new_la.source_id = man_obj.source_id
new_la.predicate_uri = 'skos:closeMatch'
new_la.object_uri = geonames_uri
new_la.creator_uuid = ''
new_la.save()
else:
print('Relation already known.')
def prepare(self):
""" checks to make sure the referrer actually exists
in the database
"""
if self.uri is not False:
ent = Entity()
found = ent.dereference(self.uri)
if found:
self.label = ent.label
self.alt_label = ent.alt_label
self.vocab_label = ent.vocabulary
self.vocab_uri = ent.vocab_uri
self.valid = True
else:
# the referring source is not known in the database
if self.vocab_uri is not False\
and self.vocab_label is not False\
and self.label is not False:
# we have enough data to save a referrer in the database
referrer_ent_type = 'vocabulary'
if self.vocab_uri != self.uri:
referrer_ent_type = 'class'
ent_v = Entity()
found_v = ent_v.dereference(self.vocab_uri)
if found_v is False:
# the referring vocabulary is not known in the database
# so we need to create it
lev = LinkEntity()
lev.uri = self.vocab_uri
lev.label = self.vocab_label
lev.alt_label = self.vocab_alt_label
lev.vocab_uri = self.vocab_uri
lev.ent_type = 'vocabulary'
lev.save()
# now are ready to make a linked entity for the referrer
le = LinkEntity()
le.uri = self.uri
le.label = self.label
le.alt_label = self.alt_label
le.vocab_uri = self.vocab_uri
le.ent_type = referrer_ent_type
le.save()
self.valid = True
def match_california_site(self, site_uuid):
""" Attempts to match California site name with a tDAR
site key word
"""
found_matches = 0
oc_item = OCitem()
exists = oc_item.check_exists(site_uuid)
if exists:
la_check = LinkAnnotation.objects\
.filter(subject=site_uuid,
predicate_uri='dc-terms:subject',
object_uri__contains=self.TDAR_VOCAB)[:1]
if exists and len(la_check) < 1:
# we don't already have a tDAR id for this item, continue with matches
# first, generate the item's JSON-LD
oc_item.generate_json_ld()
request_keywords = []
if 'oc-gen:has-obs' in oc_item.json_ld:
if isinstance(oc_item.json_ld['oc-gen:has-obs'], list):
for obs in oc_item.json_ld['oc-gen:has-obs']:
if 'oc-pred:52-alternate-site-or-place-name' in obs:
if isinstance(
obs['oc-pred:52-alternate-site-or-place-name'],
list):
for name_obj in obs[
'oc-pred:52-alternate-site-or-place-name']:
if 'xsd:string' in name_obj:
if isinstance(name_obj['xsd:string'],
str):
name_str = name_obj['xsd:string']
request_keywords.append(name_str)
print('Checking names in tDAR: ' + '; '.join(request_keywords))
for keyword in request_keywords:
tdar_api = tdarAPI()
results = tdar_api.get_site_keyword(keyword)
if isinstance(results, list):
for result in results[:self.max_results]:
# assume it is a spurious match
match_real = False
lw_result = result['label'].lower()
lw_keyword = keyword.lower()
if lw_result == lw_keyword:
# the trinomial and the tDAR result exactly match
match_real = True
if match_real:
print('FOUND ' + result['label'])
found_matches += 1
# OK! Found a match, first save the linked entity in the link entity table
le_check = False
try:
le_check = LinkEntity.objects.get(
uri=result['id'])
except LinkEntity.DoesNotExist:
le_check = False
if le_check is False:
le = LinkEntity()
le.uri = result['id']
le.label = result['label']
le.alt_label = result['label']
le.vocab_uri = self.TDAR_VOCAB
le.ent_type = 'type'
le.save()
# Now save the link annotation
la = LinkAnnotation()
la.subject = oc_item.manifest.uuid
la.subject_type = oc_item.manifest.item_type
la.project_uuid = oc_item.manifest.project_uuid
la.source_id = 'tdar-api-lookup'
la.predicate_uri = self.DC_TERMS_SUBJECT
la.object_uri = result['id']
la.save()
else:
print('Almost! ' + result['label'] +
' is not exactly: ' + keyword)
if tdar_api.request_error:
self.request_error = True
print('HTTP request to tDAR failed!')
self.error_wait += self.base_wait
if self.error_wait > self.max_wait:
print('Too many failures, quiting...')
sys.exit('Quitting process')
else:
# sleep some minutes before trying again
print('Will try again in ' + str(self.error_wait) +
' seconds...')
sleep(self.error_wait)
else:
self.request_error = False
if self.error_wait >= self.base_wait:
print('HTTP requests resumed OK, will continue.')
self.error_wait = 0
return found_matches
def match_trinomial_obj(self, tri):
""" Attempts to match a trinomial object 'tri'
against tDAR, if it hasn't yet been matched
"""
found_matches = 0
manifest = False
try:
manifest = Manifest.objects.get(uuid=tri.uuid)
except Manifest.DoesNotExist:
manifest = False
la_check = LinkAnnotation.objects\
.filter(subject=tri.uuid,
predicate_uri='dc-terms:subject',
object_uri__contains=self.TDAR_VOCAB)[:1]
if len(la_check) < 1 and manifest is not False:
# we don't already have a tDAR id for this item, continue with matches
tri_man = TrinomialManage()
request_keywords = [tri.trinomial]
if self.lead_zero_check:
# check multiple leading zeros
tri_parts = tri_man.parse_trinomial(tri.trinomial)
site = tri_parts['site']
site_part_len = len(site)
while len(site) < 4:
site = '0' + site
new_trinomial = tri_parts['state'] + tri_parts['county'] + site
request_keywords.append(new_trinomial)
for keyword in request_keywords:
tdar_api = tdarAPI()
results = tdar_api.get_site_keyword(keyword)
if isinstance(results, list):
for result in results[:self.max_results]:
# assume it is a spurious match
match_real = False
if result['label'] == tri.trinomial:
# the trinomial and the tDAR result exactly match
match_real = True
else:
# check if the only difference is in leading zeros
tri_parts = tri_man.parse_trinomial(tri.trinomial)
site = tri_parts['site']
site_part_len = len(site)
while len(site) < 5:
site = '0' + site
new_trinomial = tri_parts['state'] + tri_parts['county'] + site
if new_trinomial == result['label']:
# A good match, the tDAR result and the trinomial
# match (but with different leading zeros)
match_real = True
if match_real:
found_matches += 1
# OK! Found a match, first save the linked entity in the link entity table
le_check = False
try:
le_check = LinkEntity.objects.get(uri=result['id'])
except LinkEntity.DoesNotExist:
le_check = False
if le_check is False:
le = LinkEntity()
le.uri = result['id']
le.label = result['label']
le.alt_label = result['label']
le.vocab_uri = self.TDAR_VOCAB
le.ent_type = 'type'
le.save()
# Now save the link annotation
la = LinkAnnotation()
la.subject = tri.uuid
la.subject_type = manifest.item_type
la.project_uuid = manifest.project_uuid
la.source_id = 'tdar-api-lookup'
la.predicate_uri = self.DC_TERMS_SUBJECT
la.object_uri = result['id']
la.save()
else:
print('Almost! ' + result['label'] + ' is not exactly: ' + tri.trinomial)
if tdar_api.request_error:
self.request_error = True
print('HTTP request to tDAR failed!')
self.error_wait += self.base_wait
if self.error_wait > self.max_wait:
print('Too many failures, quiting...')
sys.exit('Quitting process')
else:
# sleep some minutes before trying again
print('Will try again in ' + str(self.error_wait) + ' seconds...')
sleep(self.error_wait)
else:
self.request_error = False
if self.error_wait >= self.base_wait:
print('HTTP requests resumed OK, will continue.')
self.error_wait = 0
return found_matches
def prepare(self):
""" checks to make sure the referrer actually exists
in the database
"""
if self.uri is not False:
ent = Entity()
found = ent.dereference(self.uri)
if found:
self.label = ent.label
self.alt_label = ent.alt_label
self.vocab_label = ent.vocabulary
self.vocab_uri = ent.vocab_uri
self.valid = True
else:
# the referring source is not known in the database
if self.vocab_uri is not False\
and self.vocab_label is not False\
and self.label is not False:
# we have enough data to save a referrer in the database
referrer_ent_type = 'vocabulary'
if self.vocab_uri != self.uri:
referrer_ent_type = 'class'
ent_v = Entity()
found_v = ent_v.dereference(self.vocab_uri)
if found_v is False:
# the referring vocabulary is not known in the database
# so we need to create it
lev = LinkEntity()
lev.uri = self.vocab_uri
lev.label = self.vocab_label
lev.alt_label = self.vocab_alt_label
lev.vocab_uri = self.vocab_uri
lev.ent_type = 'vocabulary'
lev.save()
# now are ready to make a linked entity for the referrer
le = LinkEntity()
le.uri = self.uri
le.label = self.label
le.alt_label = self.alt_label
le.vocab_uri = self.vocab_uri
le.ent_type = referrer_ent_type
le.save()
self.valid = True
def check_add_link_entity(self, uri):
""" checkes to see if an entity exists, if not, it adds
it if we recognize the URI to be part of a
known vocabulary
"""
try:
act_ent = LinkEntity.objects.get(uri=uri)
except LinkEntity.DoesNotExist:
act_ent = False
if act_ent is False:
label = False
alt_label = False
ent_type = 'class'
vocab_uri = False
if '.geonames.org' in uri:
geo_api = GeonamesAPI()
vocab_uri = GeonamesAPI().VOCAB_URI
labels = geo_api.get_labels_for_uri(uri)
if isinstance(labels, dict):
# got the label!
label = labels['label']
alt_label = labels['alt_label']
elif 'UBERON' in uri:
uber_api = uberonAPI()
vocab_uri = uberonAPI().VOCAB_URI
label = uber_api.get_uri_label_from_graph(uri)
if label is not False:
alt_label = label
elif 'eol.org' in uri:
eol_api = eolAPI()
vocab_uri = eolAPI().VOCAB_URI
labels = eol_api.get_labels_for_uri(uri)
if isinstance(labels, dict):
# got the label!
label = labels['label']
alt_label = labels['alt_label']
elif 'wikipedia.org' in uri:
# page name in the URI of the article
link_ex = uri.split('/')
label = urlunquote(link_ex[-1])
label = label.replace('_', ' ') # underscores in Wikipedia titles
alt_label = label
vocab_uri = 'http://www.wikipedia.org/'
elif 'vocab.getty.edu/aat' in uri:
print('Finding: ' + uri)
getty_api = gettyAPI()
vocab_uri = gettyAPI().VOCAB_URI
labels = getty_api.get_labels_for_uri(uri)
if isinstance(labels, dict):
# got the label!
label = labels['label']
alt_label = labels['alt_label']
elif 'numismatics.org/ocre/id/' in uri:
print('Finding: ' + uri)
ANSochre = ANSochreAPI()
vocab_uri = ANSochreAPI().VOCAB_URI
labels = ANSochre.get_labels_for_uri(uri)
if isinstance(labels, dict):
# got the label!
label = labels['label']
alt_label = labels['alt_label']
if label is not False and vocab_uri is not False:
# ok to make an entity then!
ent = LinkEntity()
ent.uri = uri
ent.label = label
ent.alt_label = alt_label
ent.vocab_uri = vocab_uri
ent.ent_type = ent_type
ent.save()
def match_california_site(self, site_uuid):
""" Attempts to match California site name with a tDAR
site key word
"""
found_matches = 0
oc_item = OCitem()
exists = oc_item.check_exists(site_uuid)
if exists:
la_check = LinkAnnotation.objects\
.filter(subject=site_uuid,
predicate_uri='dc-terms:subject',
object_uri__contains=self.TDAR_VOCAB)[:1]
if exists and len(la_check) < 1:
# we don't already have a tDAR id for this item, continue with matches
# first, generate the item's JSON-LD
oc_item.generate_json_ld()
request_keywords = []
if 'oc-gen:has-obs' in oc_item.json_ld:
if isinstance(oc_item.json_ld['oc-gen:has-obs'], list):
for obs in oc_item.json_ld['oc-gen:has-obs']:
if 'oc-pred:52-alternate-site-or-place-name' in obs:
if isinstance(obs['oc-pred:52-alternate-site-or-place-name'], list):
for name_obj in obs['oc-pred:52-alternate-site-or-place-name']:
if 'xsd:string' in name_obj:
if isinstance(name_obj['xsd:string'], str):
name_str = name_obj['xsd:string']
request_keywords.append(name_str)
print('Checking names in tDAR: ' + '; '.join(request_keywords))
for keyword in request_keywords:
tdar_api = tdarAPI()
results = tdar_api.get_site_keyword(keyword)
if isinstance(results, list):
for result in results[:self.max_results]:
# assume it is a spurious match
match_real = False
lw_result = result['label'].lower()
lw_keyword = keyword.lower()
if lw_result == lw_keyword:
# the trinomial and the tDAR result exactly match
match_real = True
if match_real:
print('FOUND ' + result['label'])
found_matches += 1
# OK! Found a match, first save the linked entity in the link entity table
le_check = False
try:
le_check = LinkEntity.objects.get(uri=result['id'])
except LinkEntity.DoesNotExist:
le_check = False
if le_check is False:
le = LinkEntity()
le.uri = result['id']
le.label = result['label']
le.alt_label = result['label']
le.vocab_uri = self.TDAR_VOCAB
le.ent_type = 'type'
le.save()
# Now save the link annotation
la = LinkAnnotation()
la.subject = oc_item.manifest.uuid
la.subject_type = oc_item.manifest.item_type
la.project_uuid = oc_item.manifest.project_uuid
la.source_id = 'tdar-api-lookup'
la.predicate_uri = self.DC_TERMS_SUBJECT
la.object_uri = result['id']
la.save()
else:
print('Almost! ' + result['label'] + ' is not exactly: ' + keyword)
if tdar_api.request_error:
self.request_error = True
print('HTTP request to tDAR failed!')
self.error_wait += self.base_wait
if self.error_wait > self.max_wait:
print('Too many failures, quiting...')
sys.exit('Quitting process')
else:
# sleep some minutes before trying again
print('Will try again in ' + str(self.error_wait) + ' seconds...')
sleep(self.error_wait)
else:
self.request_error = False
if self.error_wait >= self.base_wait:
print('HTTP requests resumed OK, will continue.')
self.error_wait = 0
return found_matches
def match_trinomial_obj(self, tri):
""" Attempts to match a trinomial object 'tri'
against tDAR, if it hasn't yet been matched
"""
found_matches = 0
manifest = False
try:
manifest = Manifest.objects.get(uuid=tri.uuid)
except Manifest.DoesNotExist:
manifest = False
la_check = LinkAnnotation.objects\
.filter(subject=tri.uuid,
predicate_uri='dc-terms:subject',
object_uri__contains=self.TDAR_VOCAB)[:1]
if len(la_check) < 1 and manifest is not False:
# we don't already have a tDAR id for this item, continue with matches
tri_man = TrinomialManage()
request_keywords = [tri.trinomial]
if self.lead_zero_check:
# check multiple leading zeros
tri_parts = tri_man.parse_trinomial(tri.trinomial)
site = tri_parts['site']
site_part_len = len(site)
while len(site) < 4:
site = '0' + site
new_trinomial = tri_parts['state'] + tri_parts[
'county'] + site
request_keywords.append(new_trinomial)
for keyword in request_keywords:
tdar_api = tdarAPI()
results = tdar_api.get_site_keyword(keyword)
if isinstance(results, list):
for result in results[:self.max_results]:
# assume it is a spurious match
match_real = False
if result['label'] == tri.trinomial:
# the trinomial and the tDAR result exactly match
match_real = True
else:
# check if the only difference is in leading zeros
tri_parts = tri_man.parse_trinomial(tri.trinomial)
site = tri_parts['site']
site_part_len = len(site)
while len(site) < 5:
site = '0' + site
new_trinomial = tri_parts['state'] + tri_parts[
'county'] + site
if new_trinomial == result['label']:
# A good match, the tDAR result and the trinomial
# match (but with different leading zeros)
match_real = True
if match_real:
found_matches += 1
# OK! Found a match, first save the linked entity in the link entity table
le_check = False
try:
le_check = LinkEntity.objects.get(
uri=result['id'])
except LinkEntity.DoesNotExist:
le_check = False
if le_check is False:
le = LinkEntity()
le.uri = result['id']
le.label = result['label']
le.alt_label = result['label']
le.vocab_uri = self.TDAR_VOCAB
le.ent_type = 'type'
le.save()
# Now save the link annotation
la = LinkAnnotation()
la.subject = tri.uuid
la.subject_type = manifest.item_type
la.project_uuid = manifest.project_uuid
la.source_id = 'tdar-api-lookup'
la.predicate_uri = self.DC_TERMS_SUBJECT
la.object_uri = result['id']
la.save()
else:
print('Almost! ' + result['label'] +
' is not exactly: ' + tri.trinomial)
if tdar_api.request_error:
self.request_error = True
print('HTTP request to tDAR failed!')
self.error_wait += self.base_wait
if self.error_wait > self.max_wait:
print('Too many failures, quiting...')
sys.exit('Quitting process')
else:
# sleep some minutes before trying again
print('Will try again in ' + str(self.error_wait) +
' seconds...')
sleep(self.error_wait)
else:
self.request_error = False
if self.error_wait >= self.base_wait:
print('HTTP requests resumed OK, will continue.')
self.error_wait = 0
return found_matches